Whole genome sequencing and characteristics of extended-spectrum beta-lactamase producing Escherichia coli isolated from poultry farms in Banaskantha, India
Worldwide dissemination of extended-spectrum -lactamase (ESBL)-producing Escherichia coli constitutes an emerging global health issue, with animal food products contributing as potential reservoirs. ESBL E. coli infection is associated with the high mortality and mobility rate in developing countrie...
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Frontiers Media S.A.
2022-10-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.996214/full |
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| author | Mitul A. Patel Aparna Pandey A. C. Patel S. S. Patel H. C. Chauhan M. D. Shrimali Pankaj A. Patel S. K. Mohapatra B. S. Chandel |
| author_facet | Mitul A. Patel Aparna Pandey A. C. Patel S. S. Patel H. C. Chauhan M. D. Shrimali Pankaj A. Patel S. K. Mohapatra B. S. Chandel |
| author_sort | Mitul A. Patel |
| collection | DOAJ |
| description | Worldwide dissemination of extended-spectrum -lactamase (ESBL)-producing Escherichia coli constitutes an emerging global health issue, with animal food products contributing as potential reservoirs. ESBL E. coli infection is associated with the high mortality and mobility rate in developing countries due to less susceptibility to antibiotics. The present study aimed to elucidate the molecular characteristics and sequence-based analysis of ESBL E. coli in the Gujarat state of India. This study included 108 E. coli strains were isolated from different poultry farms (broiler and layer) in the Banaskantha District. PCR was employed to identify genotypic ESBL-producing antimicrobial resistance genes. Overall, a high occurrence of ESBL genes was found in poultry farms due to the high usage of antimicrobials. The PCR analysis revealed that 79.62% of isolates were detected positive with one or more ESBL genes. Among them, blaTEM (63.88%) was found to be the predominant genotype, followed by blaSHV (30.55%) and blaOXA (28.70%). In the blaCTX-M group, a higher occurrence was observed in blaCTX-M-9 (23.14%), followed by blaCTX-M-2 (24.07%) and blaCTX-M-1 (22.22%). We used the whole-genome sequencing (WGS) method to evaluate the antimicrobial resistance genes, virulence factors, single nucleotide polymorphisms (SNPs), plasmid replicons, and plasmid-mediated AMR genes of one ESBL E. coli isolated. We examined the genetic relatedness of a human pathogenic E. coli strain by comparing its sequence with the broad geographical reference E. coli sequences. Escherichia coli ST 681 was determined using multi-locus sequence typing. We compared our findings to the reference sequence of Escherichia coli str. K- 12 substr. MG1655. We found 24,937 SNPs with 21,792 in the genic region, 3,145 in the intergenic region, and six InDels across the genome. The WGS analysis revealed 46 antimicrobial resistance genes and seven plasmid-mediated AMR genes viz., tetA, qnrS1, dfrA14, sul2, aph(3”)-lb, aph(6)-ld, and Aph(3’)-la. The ST 681 was found to have Cib, traT, and terC virulence factors and two plasmid replicons, IncFII(pHN7A8) and IncI1-I(Alpha). This study revealed a higher occurrence of ESBL E. coli detected in poultry. |
| first_indexed | 2024-04-11T16:49:14Z |
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| spelling | doaj.art-babd7f2c4a9d45f6a632c9e0e6c088a02022-12-22T04:13:30ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-10-011310.3389/fmicb.2022.996214996214Whole genome sequencing and characteristics of extended-spectrum beta-lactamase producing Escherichia coli isolated from poultry farms in Banaskantha, IndiaMitul A. Patel0Aparna Pandey1A. C. Patel2S. S. Patel3H. C. Chauhan4M. D. Shrimali5Pankaj A. Patel6S. K. Mohapatra7B. S. Chandel8Department of Biotechnology, Sankalchand Patel University, Visnagar, IndiaDepartment of Biochemistry, Dental College, Sankalchand Patel University, Visnagar, IndiaDepartment of Veterinary Microbiology, Veterinary College, Kamdhenu University, Sardarkushinagar, IndiaDepartment of Veterinary Microbiology, Veterinary College, Kamdhenu University, Sardarkushinagar, IndiaDepartment of Veterinary Microbiology, Veterinary College, Kamdhenu University, Sardarkushinagar, IndiaDepartment of Animal Biotechnology, Veterinary College, Kamdhenu University, Sardarkushinagar, IndiaDepartment of Physiology, Veterinary College, Kamdhenu University, Sardarkushinagar, IndiaDepartment of Animal Biotechnology, Veterinary College, Kamdhenu University, Sardarkushinagar, IndiaDepartment of Animal Biotechnology, Veterinary College, Kamdhenu University, Sardarkushinagar, IndiaWorldwide dissemination of extended-spectrum -lactamase (ESBL)-producing Escherichia coli constitutes an emerging global health issue, with animal food products contributing as potential reservoirs. ESBL E. coli infection is associated with the high mortality and mobility rate in developing countries due to less susceptibility to antibiotics. The present study aimed to elucidate the molecular characteristics and sequence-based analysis of ESBL E. coli in the Gujarat state of India. This study included 108 E. coli strains were isolated from different poultry farms (broiler and layer) in the Banaskantha District. PCR was employed to identify genotypic ESBL-producing antimicrobial resistance genes. Overall, a high occurrence of ESBL genes was found in poultry farms due to the high usage of antimicrobials. The PCR analysis revealed that 79.62% of isolates were detected positive with one or more ESBL genes. Among them, blaTEM (63.88%) was found to be the predominant genotype, followed by blaSHV (30.55%) and blaOXA (28.70%). In the blaCTX-M group, a higher occurrence was observed in blaCTX-M-9 (23.14%), followed by blaCTX-M-2 (24.07%) and blaCTX-M-1 (22.22%). We used the whole-genome sequencing (WGS) method to evaluate the antimicrobial resistance genes, virulence factors, single nucleotide polymorphisms (SNPs), plasmid replicons, and plasmid-mediated AMR genes of one ESBL E. coli isolated. We examined the genetic relatedness of a human pathogenic E. coli strain by comparing its sequence with the broad geographical reference E. coli sequences. Escherichia coli ST 681 was determined using multi-locus sequence typing. We compared our findings to the reference sequence of Escherichia coli str. K- 12 substr. MG1655. We found 24,937 SNPs with 21,792 in the genic region, 3,145 in the intergenic region, and six InDels across the genome. The WGS analysis revealed 46 antimicrobial resistance genes and seven plasmid-mediated AMR genes viz., tetA, qnrS1, dfrA14, sul2, aph(3”)-lb, aph(6)-ld, and Aph(3’)-la. The ST 681 was found to have Cib, traT, and terC virulence factors and two plasmid replicons, IncFII(pHN7A8) and IncI1-I(Alpha). This study revealed a higher occurrence of ESBL E. coli detected in poultry.https://www.frontiersin.org/articles/10.3389/fmicb.2022.996214/fullwhole genome sequencingESBLEscherichia coliantimicrobial resistanceplasmidspolymerase chain reaction |
| spellingShingle | Mitul A. Patel Aparna Pandey A. C. Patel S. S. Patel H. C. Chauhan M. D. Shrimali Pankaj A. Patel S. K. Mohapatra B. S. Chandel Whole genome sequencing and characteristics of extended-spectrum beta-lactamase producing Escherichia coli isolated from poultry farms in Banaskantha, India Frontiers in Microbiology whole genome sequencing ESBL Escherichia coli antimicrobial resistance plasmids polymerase chain reaction |
| title | Whole genome sequencing and characteristics of extended-spectrum beta-lactamase producing Escherichia coli isolated from poultry farms in Banaskantha, India |
| title_full | Whole genome sequencing and characteristics of extended-spectrum beta-lactamase producing Escherichia coli isolated from poultry farms in Banaskantha, India |
| title_fullStr | Whole genome sequencing and characteristics of extended-spectrum beta-lactamase producing Escherichia coli isolated from poultry farms in Banaskantha, India |
| title_full_unstemmed | Whole genome sequencing and characteristics of extended-spectrum beta-lactamase producing Escherichia coli isolated from poultry farms in Banaskantha, India |
| title_short | Whole genome sequencing and characteristics of extended-spectrum beta-lactamase producing Escherichia coli isolated from poultry farms in Banaskantha, India |
| title_sort | whole genome sequencing and characteristics of extended spectrum beta lactamase producing escherichia coli isolated from poultry farms in banaskantha india |
| topic | whole genome sequencing ESBL Escherichia coli antimicrobial resistance plasmids polymerase chain reaction |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.996214/full |
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